Analyzing functional similarity of protein sequences with discrete wavelet transform

Zhi-ning Wen; Ke-long Wang; Meng-long Li; Fu-sheng Nie; Yi Yang

doi:10.1016/j.compbiolchem.2005.04.007

Analyzing functional similarity of protein sequences with discrete wavelet transform

Comput Biol Chem. 2005 Jun;29(3):220-8. doi: 10.1016/j.compbiolchem.2005.04.007.

Authors

Zhi-ning Wen¹, Ke-long Wang, Meng-long Li, Fu-sheng Nie, Yi Yang

Affiliation

¹ College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.

PMID: 15979042
DOI: 10.1016/j.compbiolchem.2005.04.007

Abstract

This paper applies discrete wavelet transform (DWT) with various protein substitution models to find functional similarity of proteins with low identity. A new metric, 'S' function, based on the DWT is proposed to measure the pair-wise similarity. We also develop a segmentation technique, combined with DWT, to handle long protein sequences. The results are compared with those using the pair-wise alignment and PSI-BLAST.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence*
Amino Acid Substitution*
Computer Simulation
Structural Homology, Protein*